Re: [AMBER] Error with nmode calculations

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 5 Aug 2016 15:10:33 -0400

On Fri, Aug 5, 2016 at 2:10 PM, Praneeth Bommisetti <iampraneeth11.gmail.com
> wrote:


> *Beginning nmode calculations with
> /usr/local/amber14/bin/mmpbsa_py_nabnmode calculating complex
> contribution...Line minimizer aborted: max number of iterations reachedLine
> minimizer aborted: step at lower bound 1e-20Line minimizer
> aborted: step at lower bound 1e-20Line minimizer aborted: step
> at lower bound 1e-20Line minimizer aborted: step at lower
> bound 1e-20Line minimizer aborted: step at lower
> bound 1e-20*
> and this goes on...
>
> What does this mean, I read a similar issue on the archive but I couldn't
> get sufficient insights,
> I checked the generated trajectory files. They seem to be normal.
>

‚ÄčIt means that the minimizer was having a hard time finding a local minimum
for the potential energy function. Since normal mode calculations rely on
a local minimum in its underlying theory, this inability to minimize some
snapshots means those snapshots need to be excluded from normal mode
analysis.

HTH,
Jason

-- 
Jason M. Swails
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Received on Fri Aug 05 2016 - 12:30:02 PDT
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